In the 1987–88 campaign Begiristain helped Real finish runners-up in both league and cup, losing in both competitions to FC Barcelona. Within a month of the latter he, along with Bakero and López Rekarte, signed for the Catalan club.[2]

During seven seasons at the club Begiristain played more than 300 official matches and scored 63 goals in the league, with a career-best 15 in 1992–93 as Barça won the third of four successive titles; among his best moments were hat-tricks against Real Valladolid in 1991,[4] and Real Zaragoza two years later.[5]

In 1995, after gradually losing his importance with Barcelona (although he still registered 44 games and 13 goals in the last two seasons combined), Begiristain signed for Deportivo de La Coruña, where he linked up with two past acquaintances, Toshack and López Rekarte. He subsequently helped his new club win the Spanish Supercup, scoring in the away leg for a 2–1 win against Real Madrid at the Santiago Bernabéu.[6]

During the last season in Galicia Begiristain only appeared ten times, but scored against CF Extremadura on the final round, granting Depor a third-place finish with the 1–0 win.[7] He closed out his career in 1999 with Urawa Red Diamonds of Japan, having played in more than 500 official matches in his country and surpassing the 100-goal mark.

After retiring as a player, Begiristain worked for Televisió de Catalunya before becoming director of football at former club Barcelona,[8][9] occupying that position from 2003 until 29 June 2010: on that day he declared that, with president Joan Laporta leaving, it was the right time for him to part ways with the organization as well.[10]